Biocompatible Fe3O4 nanocrystals were synthesized through the pyrolysis of ferric acetylacetonate (Fe(acac)3) in diphenyl oxide, in the presence of ;a,co-dicarboxyl-terminated polyethylene glycol (HOOC-PEG-COOH) and oleylamine. Unusual gelification phenomena were observed from the aliquots extracted at different reaction stages after they were cooled to room temperature. By reaction time, the average size of the Fe3O4 nanocrystals was tuned from 5.8 to 11.7 nm with an equilibrium size around 11.3 nm. By increasing the gelification degree of the stock solution, the equilibrium size of the Fe3O4 nanocrystals was further increased from 11.3 to 18.9 nm. The underlying gel formation mechanism was investigated by using ultraviolet visible absorption spectroscopy and Fourier transform infrared spectroscopy. The results suggest that the complexation between HOOC-PEG-COOH and Fe(acac)(3), with the help of oleylamine, results in large molecular networks, which are responsible for the gelification of the stock solution, while the interaction between the fragment of the molecular network and Fe3O4 nanocrystal is responsible for the second gelification process observed during the early stage of reflux. To further investigate the particle growth behavior, small molecules released during the preparation were collected and analyzed by using photoelectron spectroscopy/photoionization mass spectroscopy (PES/PIMS). It was demonstrated that the pyrolysis of the Fe precursor is strongly correlated with the particle growth process. Further numerical simulations reveal that the first gelification process induced by the complexation between HOOC-PEG-COOH and Fe(acac)(3) largely alters the pyrolysis behavior of the Fe precursor; consequently, the equilibrium size of the resultant Fe3O4 nanocrystals can effectively be tuned by the gelification degree of the stock solution.